An effective method for the extraction of berberine (BER), palmatine (PAL), and jatrorrhizine (JAT) from Coscinium fenestratum by using microwave-assisted extraction (MAE) was developed in both an open (at atmospheric pressure) and closed vessel (under a pressurized condition). The extraction yields of BER yields obtained by using MAE under optimum conditions for 15 min (60% EtOH, material/solvent ratio 1.00 g:40 mL, microwave output power 300 W) in an open vessel at a boiling point of 83 degrees C (25.20 mg/g) and in a closed vessel at 160 degrees C (27.35 mg/g) were higher than those obtained using Soxhlet extraction for 8 h (24.37 mg/g) and extraction with 0.2% sulfuric acid for 24 h (21.82 mg/g). JAT (2.36 mg/g) and PAL (0.73 mg/g) extraction yields were observed to be the highest at 170 degrees C for 15 min. Extraction using water as a solvent at 160 degrees C for 15 min yielded the same level of BER amount (20.31 mg/g) as that obtained using 0.2% sulfuric acid for 24 h. This high extraction yield could be due to the alcohol-like characteristics of water at high temperature. BER degradation was observed at a temperature above 160 degrees C. An additive such as EtOH or NaCl could reduce BER degradation. MAE is more effective than conventional extraction methods with regard to the extraction time and extraction yield for extracting protoberberine alkaloids from C. fenestratum.